[gmx-users] bond-bond and bond-angle cross terms

Mark Abraham Mark.Abraham at anu.edu.au
Mon Sep 18 07:45:33 CEST 2006

Camilo Calderon wrote:
> Hi all!
> I am new to the GROMACS-world, and I am mystified.
> How do I implement the 3 body potentials advertised in sec. 4.2.8 and 
> sec. 4.2.9 of the GROMACS 3.3 manual?
> Right now I have the following:
>  [ cross_cross_bond ]
> ;ai  aj  funct  r1e  r2e  krr
> <numbers here>
>  [ cross_bond_angle ]
> ;ai aj ak funct r1e r2e r3e krt
> <more numbers here>
> when I grompp the topol.top, what I get is a Error, with a complaint 
> "invalid directive", and then a Fatal Error, with the complaint 
> "Incorrect number of parameters - found 5, expected 2 or 4."  What is 
> really tough about this is that I've been poring over the source code, 
> trying to decypher what input format ought to be - there is nothing on 
> this either in the Manual, or in the various lists!

The contents of either gmxlib/ifunc.c or kernel/ifunc.c (sorry can't 
remember which it is) may help you work out how many parameters it needs 
  - text search for CROSS, and then find the definition of the macro 
that is being used there.

Can you give us more detail from the .top file and the error messages 
grompp returns?


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